Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of vagina,lower part of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Postmenopausal Postmenopausal,postmenopausal
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-menopausal patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-menopausal patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-menopausal patients without Endometrial cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 49
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Wald Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- obesity, vaginal pH
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 2
Source: Figure 2 + Table S1
Description: Bacterial OTUs differentially enriched among Post-menopausal patients without endometrial cancer compared to Pre-menopausal patients
Abundance in Group 1: increased abundance in Post-menopausal patients
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Endometrial cancer cancer of endometrium,endometrial Ca,endometrial cancer,endometrial neoplasm,endometrium cancer,malignant endometrial neoplasm,malignant endometrium neoplasm,malignant neoplasm of endometrium,neoplasm of endometrium,primary malignant neoplasm of endometrium,tumor of endometrium,Endometrial cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Benign
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometrial cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients undergoing hysterectomy for endometrial cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 67
- Group 1 sample size Number of subjects in the case (exposed) group
- 57
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, menopause, vaginal pH
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4 + Table S2
Description: Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients
Abundance in Group 1: decreased abundance in Endometrial cancer
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Source: Figure 4 + Table S2
Description: Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients
Abundance in Group 1: increased abundance in Endometrial cancer
NCBI | Quality Control | Links |
---|---|---|
Actinomyces | ||
Arcanobacterium | ||
Campylobacter | ||
Finegoldia | ||
Fusobacterium | ||
Gallicola | ||
Lactobacillus | ||
Peptococcus | ||
Peptoniphilus | ||
Porphyromonas | ||
Prevotella | ||
Varibaculum | ||
Anaerococcus |
Revision editor(s): WikiWorks, ChiomaBlessing